BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 041302
(484 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3EF0|A Chain A, The Structure Of Fcp1, An Essential Rna Polymerase Ii Ctd
Phosphatase
Length = 372
Score = 114 bits (286), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 84/297 (28%), Positives = 141/297 (47%), Gaps = 49/297 (16%)
Query: 216 KLRPFVHTFLKEASEMFEMYIYTMGDRPYALEMAKLLDPSREYFNARVISRDDGTQRHQK 275
K RP + FL++ SE++E++IYTMG + YA E+AK++DP+ + F RV+SRDD QK
Sbjct: 75 KFRPGLAQFLQKISELYELHIYTMGTKAYAKEVAKIIDPTGKLFQDRVLSRDDSGSLAQK 134
Query: 276 GLDVVLG-QESAVLILDDTENAWTKHRDNLILMERYHFFAS------------------- 315
L + S V+++DD + W + NLI + Y FF
Sbjct: 135 SLRRLFPCDTSMVVVIDDRGDVWDWN-PNLIKVVPYEFFVGIGDINSNFLSGNREALEEQ 193
Query: 316 -----SCRQFGYHCQSLSQLRSDESELEGA--------------LASVLKVLKRIHNIFF 356
+ + + L++ ++ E EG L + KVLK IH +++
Sbjct: 194 NKERVTALELQKSERPLAKQQNALLEDEGKPTPSHTLLHNRDHELERLEKVLKDIHAVYY 253
Query: 357 DELANDLAGR-------DVRQVLKMVRGEVLKGCKLVFSHVFPTKFPADTHYLWKMAEQL 409
+E ND++ R +V ++ ++ +VLKGC+L+FS V P + + K A
Sbjct: 254 EE-ENDISSRSGNHKHANVGLIIPKMKQKVLKGCRLLFSGVIPLGVDVLSSDIAKWAMSF 312
Query: 410 GATCSIELDPSVTHVVSTDARTEKSRWAAKEAKF-LVDPRWIETANFLWQRQPEENF 465
GA ++ TH+++ RTEK + A +V W+ + W+R PE ++
Sbjct: 313 GAEVVLDFSVPPTHLIAAKIRTEKVKKAVSMGNIKVVKLNWLTESLSQWKRLPESDY 369
>pdb|3EF1|A Chain A, The Structure Of Fcp1, An Essential Rna Polymerase Ii Ctd
Phosphatase
Length = 442
Score = 78.2 bits (191), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 41/100 (41%), Positives = 61/100 (61%), Gaps = 2/100 (2%)
Query: 216 KLRPFVHTFLKEASEMFEMYIYTMGDRPYALEMAKLLDPSREYFNARVISRDDGTQRHQK 275
K RP + FL++ SE++E++IYTMG + YA E+AK++DP+ + F RV+SRDD QK
Sbjct: 83 KFRPGLAQFLQKISELYELHIYTMGTKAYAKEVAKIIDPTGKLFQDRVLSRDDSGSLAQK 142
Query: 276 GLDVVLG-QESAVLILDDTENAWTKHRDNLILMERYHFFA 314
L + S V+++DD + W NLI + Y FF
Sbjct: 143 SLRRLFPCDTSMVVVIDDRGDVW-DWNPNLIKVVPYEFFV 181
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 38/128 (29%), Positives = 66/128 (51%), Gaps = 9/128 (7%)
Query: 346 KVLKRIHNIFFDELANDLAGR-------DVRQVLKMVRGEVLKGCKLVFSHVFPTKFPAD 398
KVLK IH ++++E ND++ R +V ++ ++ +VLKGC+L+FS V P
Sbjct: 313 KVLKDIHAVYYEE-ENDISSRSGNHKHANVGLIIPKMKQKVLKGCRLLFSGVIPLGVDVL 371
Query: 399 THYLWKMAEQLGATCSIELDPSVTHVVSTDARTEKSRWAAKEAKF-LVDPRWIETANFLW 457
+ + K A GA ++ TH+++ RTEK + A +V W+ + W
Sbjct: 372 SSDIAKWAMSFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVSMGNIKVVKLNWLTESLSQW 431
Query: 458 QRQPEENF 465
+R PE ++
Sbjct: 432 KRLPESDY 439
>pdb|1TA0|A Chain A, Three-Dimensional Structure Of A Rna-Polymerase Ii Binding
Protein With Associated Ligand
Length = 197
Score = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 3/90 (3%)
Query: 218 RPFVHTFLKEASEMFEMYIYTMGDRPYALEMAKLLDPSREYFNARVISRDDGTQRHQKGL 277
RP V FL+ E+FE ++T YA +A LLD F AR+ R
Sbjct: 57 RPHVDEFLQRMGELFECVLFTASLAKYADPVADLLD-KWGAFRARLFRESCVFHRGNYVK 115
Query: 278 DVV-LGQE-SAVLILDDTENAWTKHRDNLI 305
D+ LG++ VLILD++ ++ H DN +
Sbjct: 116 DLSRLGRDLRRVLILDNSPASYVFHPDNAV 145
>pdb|3L0Y|A Chain A, Crystal Structure Of Scp1 Phosphatase D98a Mutant
pdb|3L0Y|B Chain B, Crystal Structure Of Scp1 Phosphatase D98a Mutant
Length = 184
Score = 36.6 bits (83), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 3/90 (3%)
Query: 218 RPFVHTFLKEASEMFEMYIYTMGDRPYALEMAKLLDPSREYFNARVISRDDGTQRHQKGL 277
RP V FL+ E+FE ++T YA +A LLD F AR+ R
Sbjct: 60 RPHVDEFLQRMGELFECVLFTASLAKYADPVADLLD-KWGAFRARLFRESCVFHRGNYVK 118
Query: 278 DVV-LGQE-SAVLILDDTENAWTKHRDNLI 305
D+ LG++ VLILD++ ++ H DN +
Sbjct: 119 DLSRLGRDLRRVLILDNSPASYVFHPDNAV 148
>pdb|3PGL|A Chain A, Crystal Structure Of Human Small C-Terminal Domain
Phosphatase 1 (Scp1) Bound To Rabeprazole
pdb|3PGL|B Chain B, Crystal Structure Of Human Small C-Terminal Domain
Phosphatase 1 (Scp1) Bound To Rabeprazole
Length = 180
Score = 36.2 bits (82), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 3/90 (3%)
Query: 218 RPFVHTFLKEASEMFEMYIYTMGDRPYALEMAKLLDPSREYFNARVISRDDGTQRHQKGL 277
RP V FL+ E+FE ++T YA +A LLD F AR+ R
Sbjct: 56 RPHVDEFLQRMGELFECVLFTASLAKYADPVADLLD-KWGAFRARLFRESCVFHRGNYVK 114
Query: 278 DVV-LGQE-SAVLILDDTENAWTKHRDNLI 305
D+ LG++ VLILD++ ++ H DN +
Sbjct: 115 DLSRLGRDLRRVLILDNSPASYVFHPDNAV 144
>pdb|2GHQ|A Chain A, Ctd-Specific Phosphatase Scp1 In Complex With Peptide C-
Terminal Domain Of Rna Polymerase Ii
pdb|2GHQ|B Chain B, Ctd-Specific Phosphatase Scp1 In Complex With Peptide C-
Terminal Domain Of Rna Polymerase Ii
pdb|2GHT|A Chain A, Ctd-Specific Phosphatase Scp1 In Complex With Peptide From
C-Terminal Domain Of Rna Polymerase Ii
pdb|2GHT|B Chain B, Ctd-Specific Phosphatase Scp1 In Complex With Peptide From
C-Terminal Domain Of Rna Polymerase Ii
Length = 181
Score = 36.2 bits (82), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 3/90 (3%)
Query: 218 RPFVHTFLKEASEMFEMYIYTMGDRPYALEMAKLLDPSREYFNARVISRDDGTQRHQKGL 277
RP V FL+ E+FE ++T YA +A LLD F AR+ R
Sbjct: 57 RPHVDEFLQRMGELFECVLFTASLAKYADPVADLLD-KWGAFRARLFRESCVFHRGNYVK 115
Query: 278 DVV-LGQE-SAVLILDDTENAWTKHRDNLI 305
D+ LG++ VLILD++ ++ H DN +
Sbjct: 116 DLSRLGRDLRRVLILDNSPASYVFHPDNAV 145
>pdb|2HHL|A Chain A, Crystal Structure Of The Human Small Ctd Phosphatase 3
Isoform 1
pdb|2HHL|B Chain B, Crystal Structure Of The Human Small Ctd Phosphatase 3
Isoform 1
pdb|2HHL|C Chain C, Crystal Structure Of The Human Small Ctd Phosphatase 3
Isoform 1
pdb|2HHL|D Chain D, Crystal Structure Of The Human Small Ctd Phosphatase 3
Isoform 1
Length = 195
Score = 35.8 bits (81), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 48/95 (50%), Gaps = 3/95 (3%)
Query: 218 RPFVHTFLKEASEMFEMYIYTMGDRPYALEMAKLLDPSREYFNARVISRDDGTQRHQKGL 277
RP V FL+ ++FE ++T YA +A LLD F AR+ R
Sbjct: 70 RPHVDEFLQRMGQLFECVLFTASLAKYADPVADLLD-RWGVFRARLFRESCVFHRGNYVK 128
Query: 278 DVV-LGQE-SAVLILDDTENAWTKHRDNLILMERY 310
D+ LG+E S V+I+D++ ++ H +N + ++ +
Sbjct: 129 DLSRLGRELSKVIIVDNSPASYIFHPENAVPVQSW 163
>pdb|3L0B|A Chain A, Crystal Structure Of Scp1 Phosphatase D206a Mutant
Phosphory Intermediate
pdb|3L0B|B Chain B, Crystal Structure Of Scp1 Phosphatase D206a Mutant
Phosphory Intermediate
Length = 184
Score = 33.5 bits (75), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 43/90 (47%), Gaps = 3/90 (3%)
Query: 218 RPFVHTFLKEASEMFEMYIYTMGDRPYALEMAKLLDPSREYFNARVISRDDGTQRHQKGL 277
RP V FL+ E+FE ++T YA +A LLD F AR+ R
Sbjct: 60 RPHVDEFLQRMGELFECVLFTASLAKYADPVADLLD-KWGAFRARLFRESCVFHRGNYVK 118
Query: 278 DVV-LGQE-SAVLILDDTENAWTKHRDNLI 305
D+ LG++ VLIL ++ ++ H DN +
Sbjct: 119 DLSRLGRDLRRVLILANSPASYVFHPDNAV 148
>pdb|3L0C|A Chain A, Crystal Structure Of Scp1 Phosphatase D206a Mutant With
Trap Inorganic Phosphate
pdb|3L0C|B Chain B, Crystal Structure Of Scp1 Phosphatase D206a Mutant With
Trap Inorganic Phosphate
Length = 184
Score = 33.5 bits (75), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 43/90 (47%), Gaps = 3/90 (3%)
Query: 218 RPFVHTFLKEASEMFEMYIYTMGDRPYALEMAKLLDPSREYFNARVISRDDGTQRHQKGL 277
RP V FL+ E+FE ++T YA +A LLD F AR+ R
Sbjct: 60 RPHVDEFLQRMGELFECVLFTASLAKYADPVADLLD-KWGAFRARLFRESCVFHRGNYVK 118
Query: 278 DVV-LGQE-SAVLILDDTENAWTKHRDNLI 305
D+ LG++ VLIL ++ ++ H DN +
Sbjct: 119 DLSRLGRDLRRVLILANSPASYVFHPDNAV 148
>pdb|3ED6|A Chain A, 1.7 Angstrom Resolution Crystal Structure Of Betaine
Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus
pdb|3ED6|B Chain B, 1.7 Angstrom Resolution Crystal Structure Of Betaine
Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus
pdb|3FG0|A Chain A, 1.85 Angstrom Resolution Crystal Structure Of Betaine
Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus
(Idp00699) In Complex With Nad+
pdb|3FG0|B Chain B, 1.85 Angstrom Resolution Crystal Structure Of Betaine
Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus
(Idp00699) In Complex With Nad+
pdb|3FG0|C Chain C, 1.85 Angstrom Resolution Crystal Structure Of Betaine
Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus
(Idp00699) In Complex With Nad+
pdb|3FG0|D Chain D, 1.85 Angstrom Resolution Crystal Structure Of Betaine
Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus
(Idp00699) In Complex With Nad+
pdb|3FG0|E Chain E, 1.85 Angstrom Resolution Crystal Structure Of Betaine
Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus
(Idp00699) In Complex With Nad+
pdb|3FG0|F Chain F, 1.85 Angstrom Resolution Crystal Structure Of Betaine
Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus
(Idp00699) In Complex With Nad+
pdb|3FG0|G Chain G, 1.85 Angstrom Resolution Crystal Structure Of Betaine
Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus
(Idp00699) In Complex With Nad+
pdb|3FG0|H Chain H, 1.85 Angstrom Resolution Crystal Structure Of Betaine
Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus
(Idp00699) In Complex With Nad+
Length = 520
Score = 33.1 bits (74), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 351 IHNIF--FDELANDLAGRDVRQVLKMVRGEVLKGCKLVFSHVFPTKFPADTHYLWKMAEQ 408
IHN+F F LA+ G + + +++K V + + P +P WK+A
Sbjct: 136 IHNVFMYFAGLADKDGGEMIDSPIPDTESKIVKEPVGVVTQITPWNYPL-LQASWKIAPA 194
Query: 409 LGATCSIELDPS 420
L CS+ + PS
Sbjct: 195 LATGCSLVMKPS 206
>pdb|2Q5E|A Chain A, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|B Chain B, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|C Chain C, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|D Chain D, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|E Chain E, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|F Chain F, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|G Chain G, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|H Chain H, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
Length = 187
Score = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 27/97 (27%), Positives = 45/97 (46%), Gaps = 7/97 (7%)
Query: 218 RPFVHTFLKEASEMFEMYIYTMGDRPYALEMAKLLDPSREYFNARVISRDDGTQRHQ--- 274
RP+V FL+ E+FE ++T YA + LLD F AR+ + HQ
Sbjct: 59 RPYVDEFLRRMGELFECVLFTASLAKYADPVTDLLDRCG-VFRARLFR--ESCVFHQGCY 115
Query: 275 -KGLDVVLGQESAVLILDDTENAWTKHRDNLILMERY 310
K L + LILD++ ++ H +N + ++ +
Sbjct: 116 VKDLSRLGRDLRKTLILDNSPASYIFHPENAVPVQSW 152
>pdb|1T9Z|A Chain A, Three-Dimensional Structure Of A Rna-Polymerase Ii Binding
Protein
Length = 197
Score = 32.7 bits (73), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 42/90 (46%), Gaps = 3/90 (3%)
Query: 218 RPFVHTFLKEASEMFEMYIYTMGDRPYALEMAKLLDPSREYFNARVISRDDGTQRHQKGL 277
RP V FL+ E+FE ++T YA +A LD F AR+ R
Sbjct: 57 RPHVDEFLQRXGELFECVLFTASLAKYADPVADXLD-KWGAFRARLFRESCVFHRGNYVK 115
Query: 278 DVV-LGQE-SAVLILDDTENAWTKHRDNLI 305
D+ LG++ VLI D++ ++ H DN +
Sbjct: 116 DLSRLGRDLRRVLIXDNSPASYVFHPDNAV 145
>pdb|2XNH|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 287
Score = 32.3 bits (72), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 404 KMAEQLGATCSIELDPSVTHVVSTDARTEKSRWAAKEAKFLVDPRWIETANFLWQRQPEE 463
K + G +L+ SVTH+++ + ++K AA K ++ P WI+T LW++ E+
Sbjct: 126 KYVQXXGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKT---LWEKSQEK 182
Query: 464 NF 465
Sbjct: 183 KI 184
>pdb|3OLC|X Chain X, Crystal Structure Of The N-Terminal Region Of Topbp1
Length = 298
Score = 32.3 bits (72), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 404 KMAEQLGATCSIELDPSVTHVVSTDARTEKSRWAAKEAKFLVDPRWIETANFLWQRQPEE 463
K + G +L+ SVTH+++ + ++K AA K ++ P WI+T LW++ E+
Sbjct: 126 KYVQXXGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKT---LWEKSQEK 182
Query: 464 NF 465
Sbjct: 183 KI 184
>pdb|2XNK|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|B Chain B, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|C Chain C, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|D Chain D, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 292
Score = 32.3 bits (72), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 404 KMAEQLGATCSIELDPSVTHVVSTDARTEKSRWAAKEAKFLVDPRWIETANFLWQRQPEE 463
K + G +L+ SVTH+++ + ++K AA K ++ P WI+T LW++ E+
Sbjct: 128 KYVQXXGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKT---LWEKSQEK 184
Query: 464 NF 465
Sbjct: 185 KI 186
>pdb|3LM7|A Chain A, Crystal Structure Of Duf1341 Representative, From Yersinia
Enterocolitica Subsp. Enterocolitica 8081
pdb|3LM7|B Chain B, Crystal Structure Of Duf1341 Representative, From Yersinia
Enterocolitica Subsp. Enterocolitica 8081
Length = 249
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 47/104 (45%), Gaps = 5/104 (4%)
Query: 278 DVVLGQESAVLILDDTENAWTKH--RDNLILMERYHFFASSCRQFGYHCQSLSQLRSDES 335
D ++ +A+ L D + K + L ++ Y F A +C G+ + + D
Sbjct: 142 DAIVPVTTAIAXLKDXGGSSVKFFPXNGLDSIDEYRFVAEACAATGFWLEPTGGIDLDNF 201
Query: 336 E--LEGAL-ASVLKVLKRIHNIFFDELANDLAGRDVRQVLKMVR 376
E ++ AL A V KV+ I++ D + DV+ +L +V+
Sbjct: 202 EQIVQIALDAGVTKVIPHIYSSIIDSKTGNTRPEDVKTLLDIVK 245
>pdb|3PV8|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddttp-Da In Closed
Conformation
pdb|3PV8|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddttp-Da In Closed
Conformation
pdb|3PX0|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Dctp-Da Mismatch (Tautomer) In
Closed Conformation
pdb|3PX0|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Dctp-Da Mismatch (Tautomer) In
Closed Conformation
pdb|3PX4|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Wobble) In
Ajar Conformation
pdb|3PX4|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Wobble) In
Ajar Conformation
pdb|3PX6|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Tautomer)
In Closed Conformation
pdb|3PX6|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Tautomer)
In Closed Conformation
pdb|3THV|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddatp-Dt In Closed
Conformation
pdb|3THV|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddatp-Dt In Closed
Conformation
pdb|3TI0|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddgtp-Dc In Closed
Conformation
pdb|3TI0|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddgtp-Dc In Closed
Conformation
pdb|4DSE|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DSE|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DSF|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4DSF|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
Length = 592
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 275 KGLDVVLGQESAVLILDDTENAWTKHRDNLILMERYHFFASSCRQFGYHCQSLSQLRSDE 334
K L V+L ++ + +L T+ ++ D L + YH + H + L +L+S
Sbjct: 248 KQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENI----LHYRQLGKLQS-- 301
Query: 335 SELEGALASVLKVLKRIHNIF 355
+ +EG L V K++H IF
Sbjct: 302 TYIEGLLKVVRPATKKVHTIF 322
>pdb|4DQI|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Dctp (Paired With Dg Of
Template)
pdb|4DQI|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Dctp (Paired With Dg Of
Template)
pdb|4DQP|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Ddctp (Paired With Dg Of
Template)
pdb|4DQP|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Ddctp (Paired With Dg Of
Template)
pdb|4DS4|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mn2+
pdb|4DS4|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mn2+
pdb|4DS5|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mg2+
pdb|4DS5|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mg2+
Length = 592
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 275 KGLDVVLGQESAVLILDDTENAWTKHRDNLILMERYHFFASSCRQFGYHCQSLSQLRSDE 334
K L V+L ++ + +L T+ ++ D L + YH + H + L +L+S
Sbjct: 248 KQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENI----LHYRQLGKLQS-- 301
Query: 335 SELEGALASVLKVLKRIHNIF 355
+ +EG L V K++H IF
Sbjct: 302 TYIEGLLKVVRPATKKVHTIF 322
>pdb|4DQQ|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DQQ|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DQR|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4DQR|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4E0D|A Chain A, Binary Complex Of Bacillus Dna Polymerase I Large Fragment
E658a And Duplex Dna
Length = 592
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 275 KGLDVVLGQESAVLILDDTENAWTKHRDNLILMERYHFFASSCRQFGYHCQSLSQLRSDE 334
K L V+L ++ + +L T+ ++ D L + YH + H + L +L+S
Sbjct: 248 KQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENI----LHYRQLGKLQS-- 301
Query: 335 SELEGALASVLKVLKRIHNIF 355
+ +EG L V K++H IF
Sbjct: 302 TYIEGLLKVVRPATKKVHTIF 322
>pdb|3HT3|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus V713p Mutant Bound To G:dctp
pdb|3HT3|D Chain D, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus V713p Mutant Bound To G:dctp
Length = 579
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 275 KGLDVVLGQESAVLILDDTENAWTKHRDNLILMERYHFFASSCRQFGYHCQSLSQLRSDE 334
K L V+L ++ + +L T+ ++ D L + YH + H + L +L+S
Sbjct: 235 KQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENI----LHYRQLGKLQS-- 288
Query: 335 SELEGALASVLKVLKRIHNIF 355
+ +EG L V K++H IF
Sbjct: 289 TYIEGLLKVVRPATKKVHTIF 309
>pdb|3HP6|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus F710y Mutant Bound To G:t
Mismatch
pdb|3HP6|D Chain D, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus F710y Mutant Bound To G:t
Mismatch
Length = 580
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 275 KGLDVVLGQESAVLILDDTENAWTKHRDNLILMERYHFFASSCRQFGYHCQSLSQLRSDE 334
K L V+L ++ + +L T+ ++ D L + YH + H + L +L+S
Sbjct: 236 KQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENI----LHYRQLGKLQS-- 289
Query: 335 SELEGALASVLKVLKRIHNIF 355
+ +EG L V K++H IF
Sbjct: 290 TYIEGLLKVVRPATKKVHTIF 310
>pdb|2HHW|A Chain A, Ddttp:o6-Methyl-Guanine Pair In The Polymerase Active
Site, In The Closed Conformation
pdb|2HHW|D Chain D, Ddttp:o6-Methyl-Guanine Pair In The Polymerase Active
Site, In The Closed Conformation
Length = 580
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 275 KGLDVVLGQESAVLILDDTENAWTKHRDNLILMERYHFFASSCRQFGYHCQSLSQLRSDE 334
K L V+L ++ + +L T+ ++ D L + YH + H + L +L+S
Sbjct: 236 KQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENI----LHYRQLGKLQS-- 289
Query: 335 SELEGALASVLKVLKRIHNIF 355
+ +EG L V K++H IF
Sbjct: 290 TYIEGLLKVVRPATKKVHTIF 310
>pdb|2HVH|A Chain A, Ddctp:o6meg Pair In The Polymerase Active Site (0
Position)
pdb|2HVH|D Chain D, Ddctp:o6meg Pair In The Polymerase Active Site (0
Position)
pdb|2HVI|A Chain A, Ddctp:g Pair In The Polymerase Active Site (0 Position)
pdb|2HVI|D Chain D, Ddctp:g Pair In The Polymerase Active Site (0 Position)
pdb|3EZ5|A Chain A, Cocrystal Structure Of Bacillus Fragment Dna Polymerase I
With Duplex Dna , Dctp, And Zinc (Closed Form).
pdb|3EZ5|D Chain D, Cocrystal Structure Of Bacillus Fragment Dna Polymerase I
With Duplex Dna , Dctp, And Zinc (Closed Form)
Length = 580
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 275 KGLDVVLGQESAVLILDDTENAWTKHRDNLILMERYHFFASSCRQFGYHCQSLSQLRSDE 334
K L V+L ++ + +L T+ ++ D L + YH + H + L +L+S
Sbjct: 236 KQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENI----LHYRQLGKLQS-- 289
Query: 335 SELEGALASVLKVLKRIHNIF 355
+ +EG L V K++H IF
Sbjct: 290 TYIEGLLKVVRPATKKVHTIF 310
>pdb|3KVQ|A Chain A, Crystal Structure Of Vegfr2 Extracellular Domain D7
Length = 108
Score = 30.0 bits (66), Expect = 2.9, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 37/80 (46%), Gaps = 9/80 (11%)
Query: 76 TIQERPGPTLLGNLEEKTDML-YCAEVSLEMDNCPHPGSLGGMCYRCGKRLEEESGVTFS 134
T+ ER PT+ GNLE +T + EVS P P M ++ + L E+SG+
Sbjct: 4 TVLERVAPTITGNLENQTTSIGESIEVSCTASGNPPPQI---MWFKDNETLVEDSGIVLK 60
Query: 135 YICKGLRLGNDEIDRLRNTD 154
G R N I R+R D
Sbjct: 61 ---DGNR--NLTIRRVRKED 75
>pdb|3V2A|R Chain R, Vegfr-2VEGF-A Complex Structure
Length = 772
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 37/80 (46%), Gaps = 9/80 (11%)
Query: 76 TIQERPGPTLLGNLEEKTDML-YCAEVSLEMDNCPHPGSLGGMCYRCGKRLEEESGVTFS 134
T+ ER PT+ GNLE +T + EVS P P M ++ + L E+SG+
Sbjct: 660 TVLERVAPTITGNLENQTTSIGESIEVSCTASGNPPPQI---MWFKDNETLVEDSGIVLK 716
Query: 135 YICKGLRLGNDEIDRLRNTD 154
G R N I R+R D
Sbjct: 717 ---DGNR--NLTIRRVRKED 731
>pdb|1DGJ|A Chain A, Crystal Structure Of The Aldehyde Oxidoreductase From
Desulfovibrio Desulfuricans Atcc 27774
Length = 907
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 240 GDRPYALEMAKLLDPSREYF---NARVISRDDGTQRHQKGLDVVLGQESAVLILDDTENA 296
G P + + ++ D R Y+ RV R T ++G+ V LG A L DT A
Sbjct: 579 GQIPEVMSLPEMFDKMRPYYEESKKRVKERS--TAEIKRGVGVALGVYGAGLDGPDTSEA 636
Query: 297 WTKHRDN 303
W + D+
Sbjct: 637 WVELNDD 643
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.134 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,094,173
Number of Sequences: 62578
Number of extensions: 444741
Number of successful extensions: 1056
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1037
Number of HSP's gapped (non-prelim): 28
length of query: 484
length of database: 14,973,337
effective HSP length: 103
effective length of query: 381
effective length of database: 8,527,803
effective search space: 3249092943
effective search space used: 3249092943
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)